Clinical data hydra results (primarily using Hydra_k2)
Erica Baller
3/16/2018
This script goes through demographics, clinical scores, health, and psych summaries, adds clustering information, runs statistics and makes graphs from results.
Part 1 : Read in csv.s -This script reads in demographics, clinical_scores, health and psych summaries, merges them, removes NAs, codes and separates by depression.
Part 2 : merge with hydra -It then merges these documents with hydra output (made in cbica), adding Hydra_k1 through Hydra_k10 columns (which represent the number of clusters) -The script reads in 3 different types of groups (matched, unmatched, and residualized unmatched groups), and also does all gender together as well as separating them by gender.
Part 3 : Demographics tables - Demographics tables for each group (matched, unmatched, resid) were produced
Part 4 : Graphing - Graphs were then made.
For continuous variables(age, medu1), the graphs represent means, with SEM as error bars For categorical variables (race, sex) the graphs are percentages (caucasian, male) per group, with chisq used to calculate significance
Part 5 : LM -The script then runs LM on each cognitive score (clinical_measure ~ hydra_group).
-There is a test option that does this for all clinical measures and all hydra groups, but for the remainder of the analysis, Hydra_k2 was the only classification more deeply explored.
Part 6: Visreg : Look at results of linear model graphically -Allows you to visualize each cluster by cognitive measure
Part 7 : Anova -Anovas were also run on the results of the LM of each clinical value by cluster.
Part 8 : FDR Correction -FDR correction was calculated for each clinical measure ANOVA output -A table of the results was extracted
Part 1-2: Prep (read in csvs and merge with hydra)
Part 3: Demographics
## Stratified by Cluster
## level -1 1
## n 711 376
## Race (%) Caucasian 393 ( 55.3) 155 ( 41.2)
## Non-caucasian 318 ( 44.7) 221 ( 58.8)
## Sex (%) Female 476 ( 66.9) 270 ( 71.8)
## Male 235 ( 33.1) 106 ( 28.2)
## Maternal Ed (mean (sd)) 14.14 (2.26) 13.75 (2.23)
## Age (mean (sd)) 16.11 (3.00) 15.66 (3.14)
## Depression (%) Depressed 0 ( 0.0) 376 (100.0)
## Non-depressed 711 (100.0) 0 ( 0.0)
## Cluster (%) -1 711 (100.0) 0 ( 0.0)
## 1 0 ( 0.0) 376 (100.0)
## 2 0 ( 0.0) 0 ( 0.0)
## Stratified by Cluster
## 2 p test
## n 336
## Race (%) 238 ( 70.8) <0.001
## 98 ( 29.2)
## Sex (%) 207 ( 61.6) 0.015
## 129 ( 38.4)
## Maternal Ed (mean (sd)) 14.53 (2.29) <0.001
## Age (mean (sd)) 16.66 (2.49) <0.001
## Depression (%) 336 (100.0) <0.001
## 0 ( 0.0)
## Cluster (%) 0 ( 0.0) <0.001
## 0 ( 0.0)
## 336 (100.0)## Stratified by Cluster
## level -1 1
## n 2297 376
## Race (%) Caucasian 1469 ( 64.0) 177 ( 47.1)
## Non-caucasian 828 ( 36.0) 199 ( 52.9)
## Sex (%) Female 1103 ( 48.0) 264 ( 70.2)
## Male 1194 ( 52.0) 112 ( 29.8)
## Maternal Ed (mean (sd)) 14.93 (2.45) 13.89 (2.24)
## Age (mean (sd)) 13.83 (3.72) 16.27 (2.84)
## Depression (%) Depressed 0 ( 0.0) 376 (100.0)
## Non-depressed 2297 (100.0) 0 ( 0.0)
## Cluster (%) -1 2297 (100.0) 0 ( 0.0)
## 1 0 ( 0.0) 376 (100.0)
## 2 0 ( 0.0) 0 ( 0.0)
## Stratified by Cluster
## 2 p test
## n 341
## Race (%) 218 ( 63.9) <0.001
## 123 ( 36.1)
## Sex (%) 217 ( 63.6) <0.001
## 124 ( 36.4)
## Maternal Ed (mean (sd)) 14.37 (2.31) <0.001
## Age (mean (sd)) 15.96 (2.95) <0.001
## Depression (%) 341 (100.0) <0.001
## 0 ( 0.0)
## Cluster (%) 0 ( 0.0) <0.001
## 0 ( 0.0)
## 341 (100.0)## Stratified by Cluster
## level -1 1
## n 2297 346
## Race (%) Caucasian 1469 ( 64.0) 211 ( 61.0)
## Non-caucasian 828 ( 36.0) 135 ( 39.0)
## Sex (%) Female 1103 ( 48.0) 219 ( 63.3)
## Male 1194 ( 52.0) 127 ( 36.7)
## Maternal Ed (mean (sd)) 14.93 (2.45) 14.34 (2.31)
## Age (mean (sd)) 13.83 (3.72) 16.02 (3.03)
## Depression (%) Depressed 0 ( 0.0) 346 (100.0)
## Non-depressed 2297 (100.0) 0 ( 0.0)
## Cluster (%) -1 2297 (100.0) 0 ( 0.0)
## 1 0 ( 0.0) 346 (100.0)
## 2 0 ( 0.0) 0 ( 0.0)
## Stratified by Cluster
## 2 p test
## n 371
## Race (%) 184 ( 49.6) <0.001
## 187 ( 50.4)
## Sex (%) 262 ( 70.6) <0.001
## 109 ( 29.4)
## Maternal Ed (mean (sd)) 13.92 (2.25) <0.001
## Age (mean (sd)) 16.22 (2.77) <0.001
## Depression (%) 371 (100.0) <0.001
## 0 ( 0.0)
## Cluster (%) 0 ( 0.0) <0.001
## 0 ( 0.0)
## 371 (100.0)Part 4: Including Graphs
Part 5-8: Stats: LM with visreg, anova, fdr correction
## Using cl as id variables
## [1] "CNB names and FDR correction values"## clinical_measure p_FDR_corr
## 1 mood_4factorv2 0
## 2 psychosis_4factorv2 0.02
## 3 externalizing_4factorv2 0
## 4 phobias_4factorv2 0
## 5 overall_psychopathology_4factorv2 0
